scholarly journals A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Chao Zhou ◽  
Xiaoyun Liu ◽  
Xinglei Li ◽  
Hanlin Zhou ◽  
Sijia Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Duplication ◽  
Chromatin Condensation ◽  
Expression Patterns ◽  
Rice Genome ◽  
Genome Doubling ◽  
Autotetraploid Rice ◽  
A Genome ◽  
Ideal System ◽  
Accessible Chromatin

AbstractEvolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.

scholarly journals Limit cycle dynamics can guide the evolution of gene regulatory networks towards point attractors

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stuart P. Wilson ◽  
Sebastian S. James ◽  
Daniel J. Whiteley ◽  
Leah A. Krubitzer
Keyword(s):  
Gene Expression ◽  
Limit Cycles ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Specific Gene ◽  
Boolean Models ◽  
A Genome ◽  
Order Of Magnitude ◽  
Accelerate Evolution

AbstractDevelopmental dynamics in Boolean models of gene networks self-organize, either into point attractors (stable repeating patterns of gene expression) or limit cycles (stable repeating sequences of patterns), depending on the network interactions specified by a genome of evolvable bits. Genome specifications for dynamics that can map specific gene expression patterns in early development onto specific point attractor patterns in later development are essentially impossible to discover by chance mutation alone, even for small networks. We show that selection for approximate mappings, dynamically maintained in the states comprising limit cycles, can accelerate evolution by at least an order of magnitude. These results suggest that self-organizing dynamics that occur within lifetimes can, in principle, guide natural selection across lifetimes.

scholarly journals Genome-Wide Characterisation of Gene Expression in Rice Leaf Blades at 25°C and 30°C

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Zhi-guo E ◽  
Lei Wang ◽  
Ryan Qin ◽  
Haihong Shen ◽  
Jianhua Zhou
Keyword(s):  
Gene Expression ◽  
Rice Genome ◽  
Rice Seedling ◽  
Rice Leaf ◽  
Genome Wide ◽  
A Genome ◽  
Rice Samples ◽  
Low Levels ◽  
Seedling Leaf ◽  
Generation Sequencing

Rice growth is greatly affected by temperature. To examine how temperature influences gene expression in rice on a genome-wide basis, we utilised recently compiled next-generation sequencing datasets and characterised a number of RNA-sequence transcriptome samples in rice seedling leaf blades at 25°C and 30°C. Our analysis indicated that 50.4% of all genes in the rice genome (28,296/56,143) were expressed in rice samples grown at 25°C, whereas slightly fewer genes (50.2%; 28,189/56,143) were expressed in rice leaf blades grown at 30°C. Among the genes that were expressed, approximately 3% were highly expressed, whereas approximately 65% had low levels of expression. Further examination demonstrated that 821 genes had a twofold or higher increase in expression and that 553 genes had a twofold or greater decrease in expression at 25°C. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the ribosome pathway and multiple metabolic pathways were upregulated at 25°C. Based on these results, we deduced that gene expression at both transcriptional and translational levels was stimulated at 25°C, perhaps in response to a suboptimal temperature condition. Finally, we observed that temperature markedly regulates several super-families of transcription factors, including bZIP, MYB, and WRKY.

scholarly journals Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Xin Du ◽  
Leng Han ◽  
An-Yuan Guo ◽  
Zhongming Zhao
Keyword(s):  
Gene Expression ◽  
Methylation Level ◽  
Cpg Island ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Gc Content ◽  
Gene Markers ◽  
A Genome ◽  
Genome Level ◽  
Lower Ratio

CpG islands are typically located in the 5′end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones’ algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.’s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.

scholarly journals Global insights into homoeolog gene expression in upland cotton under intraspecific hybridization

2021 ◽  
Author(s):  
Kashif Shahzad ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Upland Cotton ◽  
Expression Patterns ◽  
Yield Potential ◽  
World Cotton ◽  
Intraspecific Hybridization ◽  
Genome Doubling ◽  
Gene Pairs ◽  
Agronomic Crops ◽  
Metabolic Genes

Abstract Background: Hybridization is useful to enhance yield potential of agronomic crops in the world. Cotton has genome doubling due to alloteraploidy process and hybridization process in coordinate with duplicated genome can produce more yield and adaptability. Therefore, expression of homoeolog gene pairs between hybrids and inbred parents are vital to characterize genetic source of heterosis in cotton.Results: Investigation results of homoeolog gene pairs between two contrasting hybrids and their respective inbred parents identified 36853 homoeolog genes in hybrids. It was observed both high and low hybrids had similar trends in homoeolog gene expression patterns in each tissue under study. An average of 96% of homoeolog genes had no biased expression and their expressions were derived from the equal contribution of both parents. Besides, very few homoeolog genes (An average of 1%) showed no biased or novel expression in both hybrids. The functional analysis described secondary metabolic pathways had a majority of novel biased homoeolog genes in hybrids. Conclusions: These results contribute preliminary knowledge about how hybridization affects expression patterns of homoeolog gene pairs in upland cotton hybrids. Our study also highlights the functional genomics of metabolic genes to explore the genetic mechanism of heterosis in cotton.

scholarly journals The Potential Role of Genetic Assimilation during Maize Domestication

2017 ◽  
Author(s):  
Anne Lorant ◽  
Sarah Pedersen ◽  
Irene Holst ◽  
Matthew B. Hufford ◽  
Klaus Winter ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Potential Role ◽  
Expression Patterns ◽  
Genetic Assimilation ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Maize Domestication

ABSTRACTDomestication research has largely focused on identification of morphological and genetic differences between extant populations of crops and their wild relatives. Little attention has been paid to the potential effects of environment despite substantial known changes in climate from the time of domestication to modern day. Recent research, in which maize and teosinte (i.e., wild maize) were exposed to environments similar to the time of domestication, resulted in a plastic induction of domesticated phenotypes in teosinte and little response to environment in maize. These results suggest that early agriculturalists may have selected for genetic mechanisms that cemented domestication phenotypes initially induced by a plastic response of teosinte to environment, a process known as genetic assimilation. To better understand this phenomenon and the potential role of environment in maize domestication, we examined differential gene expression in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) between past and present conditions. We identified a gene set of over 2000 loci showing a change in expression across environmental conditions in teosinte and invariance in maize. In fact, overall we observed both greater plasticity in gene expression and more substantial re-wiring of expression networks in teosinte across environments when compared to maize. While these results suggest genetic assimilation played at least some role in domestication, genes showing expression patterns consistent with assimilation are not significantly enriched for previously identified domestication candidates, indicating assimilation did not have a genome-wide effect.

scholarly journals Genome-Wide Phylogenetic Analysis, Expression Pattern, and Transcriptional Regulatory Network of the Pig C/EBP Gene Family

2021 ◽  
Vol 17 ◽  
pp. 117693432110413
Author(s):  
Chaoxin Zhang ◽  
Tao Wang ◽  
Tongyan Cui ◽  
Shengwei Liu ◽  
Bing Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Phylogenetic Analysis ◽  
Regulatory Network ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Genome Wide ◽  
A Genome

The CCAAT/enhancer binding protein (C/EBP) transcription factors (TFs) regulate many important biological processes, such as energy metabolism, inflammation, cell proliferation etc. A genome-wide gene identification revealed the presence of a total of 99 C/EBP genes in pig and 19 eukaryote genomes. Phylogenetic analysis showed that all C/EBP TFs were classified into 6 subgroups named C/EBPα, C/EBPβ, C/EBPδ, C/EBPε, C/EBPγ, and C/EBPζ. Gene expression analysis showed that the C/EBPα, C/EBPβ, C/EBPδ, C/EBPγ, and C/EBPζ genes were expressed ubiquitously with inconsistent expression patterns in various pig tissues. Moreover, a pig C/EBP regulatory network was constructed, including C/EBP genes, TFs and miRNAs. A total of 27 feed-forward loop (FFL) motifs were detected in the pig C/EBP regulatory network. Based on the RNA-seq data, gene expression patterns related to FFL sub-network were analyzed in 27 adult pig tissues. Certain FFL motifs may be tissue specific. Functional enrichment analysis indicated that C/EBP and its target genes are involved in many important biological pathways. These results provide valuable information that clarifies the evolutionary relationships of the C/EBP family and contributes to the understanding of the biological function of C/EBP genes.

Genomic and epigenomic active vitamin Dresponses in human colonic organoids

2021 ◽  
Author(s):  
Jinchao Li ◽  
David Witonsky ◽  
Emily Sprague ◽  
Dereck Alleyne ◽  
Margaret C Bielski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Differentially Expressed Genes ◽  
Chromatin Accessibility ◽  
Differentially Expressed ◽  
Active Vitamin ◽  
Host Environment ◽  
Genome Wide ◽  
Ideal System ◽  
Accessible Chromatin

Background & Aims: Active vitamin D, 1α,25(OH)2D3, is a nuclear hormone with roles in colonic homeostasis and carcinogenesis; yet, mechanisms underlying these effects are incompletely understood. Organoids are an ideal system to study genomic and epigenomic host-environment interactions. We utilize colonic organoids to measure 1α,25(OH)2D3 responses on genome-wide gene expression and chromatin accessibility over time. Methods: Human colonic organoids were treated in triplicate with 100nM 1α,25(OH)2D3 or vehicle control for 4 and 18 hours (h) for chromatin accessibility, and 6 and 24h for gene expression. ATAC- and RNA-sequencing were performed. Differentially accessible peaks were analyzed using DiffBind and EdgeR; differentially expressed genes were analyzed using DESeq2. Motif enrichment was determined using HOMER. Results: At 6h and 24h, 2870 and 2721 differentially expressed genes, respectively (false discovery rate, FDR<5%) were identified with overall stronger responses with 1α,25(OH)2D3. Vitamin D treatment led to stronger chromatin accessibility especially at 4h. The vitamin D receptor (VDR) motif was strongly enriched among accessible chromatin peaks with 1α,25(OH)2D3 treatment accounting for 30.5% and 11% of target sequences at 4h and 18h, respectively (FDR<1%). Genes such as CYP24A1, FGF19, MYC, FOS and TGFBR2 showed significant transcriptional and chromatin accessibility responses to 1α,25(OH)2D3 treatment with accessible chromatin located distant from promoters for some gene regions. Conclusions: Assessment of chromatin accessibility and transcriptional responses to 1α,25(OH)2D3 yielded new observations about vitamin D genome-wide effects in the colon facilitated by application of human colonic organoids. This framework can be applied to study host-environment interactions between individuals and populations in future.

scholarly journals A genome-wide transcriptional analysis of morphology determination inCandida albicans

2013 ◽  
Vol 24 (3) ◽  
pp. 246-260 ◽  
Author(s):  
Patricia L. Carlisle ◽  
David Kadosh
Keyword(s):  
Gene Expression ◽  
Fungal Infections ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Transcriptional Analysis ◽  
Specific Gene ◽  
Genome Wide ◽  
A Genome ◽  
Genetically Manipulated

Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship among global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated with hyphae and are generally expressed at lower levels. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition involves not only down-regulation of known hyphal-specific, genes but also differential expression of additional genes that have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide expression patterns important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.

scholarly journals Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic

2019 ◽  
Vol 116 (30) ◽  
pp. 14995-15000 ◽  
Author(s):  
Justyna Cholewa-Waclaw ◽  
Ruth Shah ◽  
Shaun Webb ◽  
Kashyap Chhatbar ◽  
Bernard Ramsahoye ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rett Syndrome ◽  
Transcription Initiation ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
A Genome ◽  
The Impact

Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here, we integrate quantitative, multidimensional experimental analysis and mathematical modeling to indicate that MeCP2 is a global transcriptional regulator whose binding to DNA creates “slow sites” in gene bodies. We hypothesize that waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shockwaves in nonequilibrium physics transport models. This mechanism differs from conventional gene-regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene-expression patterns are choreographed.

scholarly journals Genome organization is a major component of gene expression control in response to stress and during the cell division cycle in trypanosomes

Open Biology ◽  
2012 ◽  
Vol 2 (4) ◽  
pp. 120033 ◽  
Author(s):  
S. Kelly ◽  
S. Kramer ◽  
A. Schwede ◽  
P. K. Maini ◽  
K. Gull ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Division ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Expression Patterns ◽  
Cell Division Cycle ◽  
Control Of Gene Expression ◽  
Polycistronic Transcription ◽  
A Genome ◽  
Gene Expression Control

The trypanosome genome is characterized by RNA polymerase II-driven polycistronic transcription of protein-coding genes. Ten to hundreds of genes are co-transcribed from a single promoter; thus, selective regulation of individual genes via initiation is impossible. However, selective responses to external stimuli occur and post-transcriptional mechanisms are thought to account for all temporal gene expression patterns. We show that genes encoding mRNAs that are differentially regulated during the heat-shock response are selectively positioned in polycistronic transcription units; downregulated genes are close to transcription initiation sites and upregulated genes are distant. We demonstrate that the position of a reporter gene within a transcription unit is sufficient to reproduce this effect. Analysis of gene ontology annotations reveals that positional bias is not restricted to stress–response genes and that there is a genome-wide organization based on proximity to transcription initiation sites. Furthermore, we show that the relative abundance of mRNAs at different time points in the cell division cycle is dependent on the location of the corresponding genes to transcription initiation sites. This work provides evidence that the genome in trypanosomes is organized to facilitate co-coordinated temporal control of gene expression in the absence of selective promoters.

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