scholarly journals Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

2020 ◽  
Vol 12 (11) ◽  
pp. 1994-2001 ◽  
Author(s):  
Michele Wyler ◽  
Christoph Stritt ◽  
Jean-Claude Walser ◽  
Célia Baroux ◽  
Anne C Roulin
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transposable Elements ◽  
Brachypodium Distachyon ◽  
Large Fraction ◽  
Expression Patterns ◽  
Specific Gene ◽  
Differential Gene ◽  
The Relationship ◽  
Silent State

Abstract Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.

scholarly journals Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon

2020 ◽  
Author(s):  
Michele Wyler ◽  
Christoph Stritt ◽  
Jean-Claude Walser ◽  
Célia Baroux ◽  
Anne C. Roulin
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transposable Elements ◽  
Plant Species ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Small Subset ◽  
Molecular Evidence ◽  
Specific Gene ◽  
Plant Genomes

AbstractTransposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.Significance statementTransposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.

scholarly journals Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance

2021 ◽  
Author(s):  
Agata Tyczewska ◽  
Joanna Gracz-Bernaciak ◽  
Jakub Szymkowiak ◽  
Tomasz Twardowski
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zea Mays ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Differential Susceptibility ◽  
Inbred Lines ◽  
Specific Gene ◽  
Genes Encoding ◽  
Shock Proteins

AbstractDNA methylation plays a crucial role in the regulation of gene expression, activity of transposable elements, defense against foreign DNA, and inheritance of specific gene expression patterns. The link between stress exposure and sequence-specific changes in DNA methylation was hypothetical until it was shown that stresses can induce changes in the gene expression through hypomethylation or hypermethylation of DNA. To detect changes in DNA methylation under herbicide stress in two local Zea mays inbred lines exhibiting differential susceptibility to Roundup®, the methylation-sensitive amplified polymorphism (MSAP) technique was used. The overall DNA methylation levels were determined at approximately 60% for both tested lines. The most significant changes were observed for the more sensitive Z. mays line, where 6 h after the herbicide application, a large increase in the level of DNA methylation (attributed to the increase in fully methylated bands (18.65%)) was noted. DNA sequencing revealed that changes in DNA methylation profiles occurred in genes encoding heat shock proteins, membrane proteins, transporters, kinases, lipases, methyltransferases, zinc-finger proteins, cytochromes, and transposons. Herbicide stress-induced changes depended on the Z. mays variety, and the large increase in DNA methylation level in the sensitive line resulted in a lower ability to cope with stress conditions.

Maternal oxytocin administration modulates gene expression in the brains of perinatal mice

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Frances F. Hsieh ◽  
Ilya Korsunsky ◽  
Andrew J. Shih ◽  
Matthew A. Moss ◽  
Prodyot K. Chatterjee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neurite Outgrowth ◽  
Quantitative Pcr ◽  
Expression Patterns ◽  
Specific Gene ◽  
Neonatal Brain ◽  
Real Time Quantitative Pcr ◽  
Brain Gene Expression ◽  
Gene Expression Analyses ◽  
Differential Gene

Abstract Objectives Oxytocin (OXT) is widely used to facilitate labor. However, little is known about the effects of perinatal OXT exposure on the developing brain. We investigated the effects of maternal OXT administration on gene expression in perinatal mouse brains. Methods Pregnant C57BL/6 mice were treated with saline or OXT at term (n=6–7/group). Dams and pups were euthanized on gestational day (GD) 18.5 after delivery by C-section. Another set of dams was treated with saline or OXT (n=6–7/group) and allowed to deliver naturally; pups were euthanized on postnatal day 9 (PND9). Perinatal/neonatal brain gene expression was determined using Illumina BeadChip Arrays and real time quantitative PCR. Differential gene expression analyses were performed. In addition, the effect of OXT on neurite outgrowth was assessed using PC12 cells. Results Distinct and sex-specific gene expression patterns were identified in offspring brains following maternal OXT administration at term. The microarray data showed that female GD18.5 brains exhibited more differential changes in gene expression compared to male GD18.5 brains. Specifically, Cnot4 and Frmd4a were significantly reduced by OXT exposure in male and female GD18.5 brains, whereas Mtap1b, Srsf11, and Syn2 were significantly reduced only in female GD18.5 brains. No significant microarray differences were observed in PND9 brains. By quantitative PCR, OXT exposure reduced Oxtr expression in female and male brains on GD18.5 and PND9, respectively. PC12 cell differentiation assays revealed that OXT induced neurite outgrowth. Conclusions Prenatal OXT exposure induces sex-specific differential regulation of several nervous system-related genes and pathways with important neural functions in perinatal brains.

scholarly journals Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning

2021 ◽  
Author(s):  
Elizabeth Ing-Simmons ◽  
Roshan Vaid ◽  
Xin Yang Bing ◽  
Michael Levine ◽  
Mattias Mannervik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Expression Patterns ◽  
Chromatin Organization ◽  
Specific Gene ◽  
Chromatin Conformation ◽  
Dorsoventral Patterning ◽  
Tissue Specific ◽  
Cell Type Specific ◽  
The Relationship

AbstractThe relationship between chromatin organization and gene regulation remains unclear. While disruption of chromatin domains and domain boundaries can lead to misexpression of developmental genes, acute depletion of regulators of genome organization has a relatively small effect on gene expression. It is therefore uncertain whether gene expression and chromatin state drive chromatin organization or whether changes in chromatin organization facilitate cell-type-specific activation of gene expression. Here, using the dorsoventral patterning of the Drosophila melanogaster embryo as a model system, we provide evidence for the independence of chromatin organization and dorsoventral gene expression. We define tissue-specific enhancers and link them to expression patterns using single-cell RNA-seq. Surprisingly, despite tissue-specific chromatin states and gene expression, chromatin organization is largely maintained across tissues. Our results indicate that tissue-specific chromatin conformation is not necessary for tissue-specific gene expression but rather acts as a scaffold facilitating gene expression when enhancers become active.

scholarly journals JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics

2020 ◽  
Author(s):  
Russell Littman ◽  
Zachary Hemminger ◽  
Robert Foreman ◽  
Douglas Arneson ◽  
Guanglin Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Spatial Organization ◽  
Expression Patterns ◽  
Granular Cell ◽  
Detection Sensitivity ◽  
Cell Segmentation ◽  
Specific Gene ◽  
Cell Type ◽  
Differential Gene

AbstractRNA hybridization based spatial transcriptomics provides unparalleled detection sensitivity. However, inaccuracies in segmentation of image volumes into cells cause misassignment of mRNAs which is a major source of errors. Here we develop JSTA, a computational framework for Joint cell Segmentation and cell Type Annotation that utilizes prior knowledge of cell-type specific gene expression. Simulation results show that leveraging existing cell type taxonomy increases RNA assignment accuracy by more than 45%. Using JSTA we were able to classify cells in the mouse hippocampus into 133 (sub)types revealing the spatial organization of CA1, CA3, and Sst neuron subtypes. Analysis of within cell subtype spatial differential gene expression of 80 candidate genes identified 43 with statistically significant spatial differential gene expression across 61 (sub)types. Overall, our work demonstrates that known cell type expression patterns can be leveraged to improve the accuracy of RNA hybridization based spatial transcriptomics while providing highly granular cell (sub)type information. The large number of newly discovered spatial gene expression patterns substantiates the need for accurate spatial transcriptomics measurements that can provide information beyond cell (sub)type labels.

scholarly journals Changes in DNA Methylation in Response to 6-Benzylaminopurine Affect Allele-Specific Gene Expression in Populus tomentosa

2020 ◽  
Author(s):  
Anran Xuan ◽  
Yuepeng Song ◽  
Chenhao Bu ◽  
Panfei Chen ◽  
Yousry A. El-Kassaby ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Patterns ◽  
Populus Tomentosa ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Snp Analysis ◽  
Specific Gene Expression ◽  
Genome Wide ◽  
Allele Specific

The cytokinins play important roles in plant growth and development by regulating gene expression at genome wide level. DNA methylation is responsive to the external environment, but whether DNA methylation changes in response to cytokinin treatment to regulate gene expression is still unclear. Here, we used bisulfite sequencing and RNA sequencing to examine genome-wide DNA methylation and gene expression patterns in poplar (Populus tomentosa) after treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA). We identified 566 significantly differentially methylated regions (DMRs) in response to 6-BA treatment. Transcriptome analysis showed that 501 protein-coding genes, 262 long non-coding RNAs, and 15,793 24-nt small interfering RNAs were differentially expressed under 6-BA treatment. Among these, 79% were differentially expressed between alleles in P. tomentosa. Combined DNA methylation and gene expression analysis demonstrated that DNA methylation plays an important role in regulating allele-specific gene expression. To further investigate the relationship between these 6-BA-responsive genes and phenotypic variation, we performed SNP analysis of 507 6-BA-responsive DMRs via re-sequencing using a natural population of P. tomentosa and identified 206 SNPs that were significantly associated with growth and wood properties. Association analysis indicated that 53% of loci with allele-specific expression had primarily dominant effects on poplar traits. Our comprehensive analyses of P. tomentosa DNA methylation and the regulation of allele-specific gene expression suggest that DNA methylation is an important regulator of imbalanced expression between allelic loci.

scholarly journals CG methylation covaries with differential gene expression between leaf and floral bud tissues of Brachypodium distachyon

2015 ◽  
Author(s):  
Kyria Roessler ◽  
Shohei Takuno ◽  
Brandon Gaut
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sequence Data ◽  
Brachypodium Distachyon ◽  
Grass Species ◽  
Specific Gene ◽  
Specific Expression ◽  
Tissue Specific ◽  
Model Grass ◽  
Floral Bud

DNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass species Brachypodium distachyon. Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.

scholarly journals Differential gene expression in Drosophila melanogaster and D. nigrosparsa infected with the same Wolbachia strain

2020 ◽  
Author(s):  
Matsapume Detcharoen ◽  
Martin P. Schilling ◽  
Wolfgang Arthofer ◽  
Birgit C. Schlick-Steiner ◽  
Florian M. Steiner
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Differential Gene Expression ◽  
Expression Patterns ◽  
Specific Gene ◽  
Positive Effects ◽  
Arthropod Species ◽  
Expression Of Genes ◽  
Novel Host ◽  
Differential Gene

AbstractWolbachia, maternally inherited endosymbionts, infect nearly half of all arthropod species. Wolbachia manipulate their hosts to maximize their transmission, but they can also provide benefits such as nutrients and resistance to viruses for their hosts. The Wolbachia strain wMel was recently found to increase locomotor activities and possibly trigger cytoplasmic incompatibility in the fly Drosophila nigrosparsa. Here, we compared differential gene expression in Drosophila melanogaster (original host) and D. nigrosparsa (novel host), both uninfected and infected with wMel, using RNA sequencing to see if the two Drosophila species respond to the infection in the same or different ways. A total of 2164 orthologous genes were used. We found species-specific gene expression patterns. Significant changes shared by the fly species were confined to the expression of genes involved in heme binding and oxidation-reduction; the two host species differently changed the expression of genes when infected. Some of the genes were down-regulated in the infected D. nigrosparsa, which might indicate small positive effects of Wolbachia. We discuss our findings also in the light of how Wolbachia survive within both the native and the novel host.

scholarly journals Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes

2018 ◽  
Author(s):  
Annabel Ebbing ◽  
Abel Vertesy ◽  
Marco Betist ◽  
Bastiaan Spanjaard ◽  
Jan Philipp Junker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reproductive Tract ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Comprehensive Overview ◽  
Tissue Specific ◽  
C Elegans ◽  
Differential Gene ◽  
Fertility Genes

SummaryTo advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used RNA tomography to generate the first high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region and tissue-specific genes. Moreover, by combining pattern-based analysis with differential gene expression analysis, we have found extensive sex-specific gene expression differences in the germline and sperm. We have also identified genes that are specifically expressed in the male reproductive tract, including a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying novel tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, which opens up new possibilities for transcriptome-wide comparisons of gene expression patterns.

A Global Vista of the Epigenomic State of the Mouse Submandibular Gland

2021 ◽  
pp. 002203452110120
Author(s):  
C. Gluck ◽  
S. Min ◽  
A. Oyelakin ◽  
M. Che ◽  
E. Horeth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Submandibular Salivary Gland ◽  
Data Sets ◽  
Control Mechanisms ◽  
Chromatin Immunoprecipitation Sequencing

The parotid, submandibular, and sublingual glands represent a trio of oral secretory glands whose primary function is to produce saliva, facilitate digestion of food, provide protection against microbes, and maintain oral health. While recent studies have begun to shed light on the global gene expression patterns and profiles of salivary glands, particularly those of mice, relatively little is known about the location and identity of transcriptional control elements. Here we have established the epigenomic landscape of the mouse submandibular salivary gland (SMG) by performing chromatin immunoprecipitation sequencing experiments for 4 key histone marks. Our analysis of the comprehensive SMG data sets and comparisons with those from other adult organs have identified critical enhancers and super-enhancers of the mouse SMG. By further integrating these findings with complementary RNA-sequencing based gene expression data, we have unearthed a number of molecular regulators such as members of the Fox family of transcription factors that are enriched and likely to be functionally relevant for SMG biology. Overall, our studies provide a powerful atlas of cis-regulatory elements that can be leveraged for better understanding the transcriptional control mechanisms of the mouse SMG, discovery of novel genetic switches, and modulating tissue-specific gene expression in a targeted fashion.

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