scholarly journals MiRNA-mediated Changes in DNA Methylation Affect the Expression of Genes Involved in the Thickness of Pod Canopy Trait in Brassica Napus

2021 ◽  
Author(s):  
Zhiyou Chen ◽  
Ledong Jia ◽  
Yuanyuan Wan ◽  
Jinqi Ma ◽  
Kun Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Flower Buds ◽  
Promoter Regions ◽  
Flower Bud ◽  
Stem Apex ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Family Protein ◽  
Crop Development

Abstract Background: Methylation plays an important role in regulating crop development, but little is known about how methylation regulates plant architecture in rapeseed (Brassica napus). Here, we examined how methylation affects the TPC (thickness of pod canopy) trait in rapeseed by performing genome-wide methylation analysis of two extreme TPC lines. Results: We detected significant differences in overall methylation levels between the high- and low-TPC lines in the CG, CHG, and CHH contexts in the promoters of genes in the stem apex and flower bud. In flower buds, 26 genes had significantly higher methylation levels in the high-TPC samples compared to the low-TPC samples, resulting in significantly reduced gene expression. By contrast, in the stem apex samples, the promoter regions of 22 genes were hypermethylated in the high- vs. low-TPC samples. The promoters of 19 and 21 genes had significantly reduced methylation levels in the flower bud and stem apex, respectively, of the high- vs. low-TPC samples, resulting in significantly higher expression levels. Some of these differentially expressed genes are associated with TPC-related traits, such as BnaC03g53050D (UBC32), BnaA05g26660D (CYSB), BnaA10g07880D (TCP 1), BnaAnng09670D (SMP1), BnaA09g02000D (SDH2-2), BnaC01g12960D (NRT1.8), and BnaC09g30490D (TAF15b). In addition, 14 important genes related to growth and development were differentially regulated between the two groups due to miRNA-mediated differences in methylation levels in their promoters. For example, hypermethylation in the promoter region of BnaCnng64040D (Lipase family protein) mediated by miR159a led to significantly reduced gene expression in flower buds of high-TPC vs. low-TPC lines. Conclusions: These results, together with our previously generated RNA-seq and miRNA profiling data, indicate that both methylation and miRNAs are involved in regulating the expression of genes in nitrogen-related metabolic pathways, thereby affecting the TPC trait in B. napus, providing a reference for uncovering the molecular mechanism regulating this crucial trait.

scholarly journals Impact of Chromosome Fusions on 3D Genome Organization and Gene Expression in Budding Yeast

Genetics ◽  
2020 ◽  
Vol 214 (3) ◽  
pp. 651-667 ◽  
Author(s):  
Marco Di Stefano ◽  
Francesca Di Giovanni ◽  
Vasilisa Pozharskaia ◽  
Mercè Gomar-Alba ◽  
Davide Baù ◽  
...  
Keyword(s):  
Gene Expression ◽  
Budding Yeast ◽  
Nuclear Organization ◽  
Nuclear Periphery ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
3D Genome ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Chromosome Fusions

The three-dimensional (3D) organization of chromosomes can influence transcription. However, the frequency and magnitude of these effects remain debated. To determine how changes in chromosome positioning affect transcription across thousands of genes with minimal perturbation, we characterized nuclear organization and global gene expression in budding yeast containing chromosome fusions. We used computational modeling and single-cell imaging to determine chromosome positions, and integrated these data with genome-wide transcriptional profiles from RNA sequencing. We find that chromosome fusions dramatically alter 3D nuclear organization without leading to strong genome-wide changes in transcription. However, we observe a mild but significant and reproducible increase in the expression of genes displaced away from the periphery. The increase in transcription is inversely proportional to the propensity of a given locus to be at the nuclear periphery; for example, a 10% decrease in the propensity of a gene to reside at the nuclear envelope is accompanied by a 10% increase in gene expression. Modeling suggests that this is due to both deletion of telomeres and to displacement of genes relative to the nuclear periphery. These data suggest that basal transcriptional activity is sensitive to radial changes in gene position, and provide insight into the functional relevance of budding yeast chromosome-level 3D organization in gene expression.

scholarly journals Genome-Wide Relationships between TAF1 and Histone Acetyltransferases in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (7) ◽  
pp. 2791-2802 ◽  
Author(s):  
Melissa Durant ◽  
B. Franklin Pugh
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Histone Acetylation ◽  
Rna Polymerase Ii ◽  
Histone Acetyltransferases ◽  
Histone H4 ◽  
Promoter Regions ◽  
Genome Wide ◽  
Acetylated Histone H4

ABSTRACT Histone acetylation regulates gene expression, yet the functional contributions of the numerous histone acetyltransferases (HATs) to gene expression and their relationships with each other remain largely unexplored. The central role of the putative HAT-containing TAF1 subunit of TFIID in gene expression raises the fundamental question as to what extent, if any, TAF1 contributes to acetylation in vivo and to what extent it is redundant with other HATs. Our findings herein do not support the basic tenet that TAF1 is a major HAT in Saccharomyces cerevisiae, nor do we find that TAF1 is functionally redundant with other HATs, including Gcn5, Elp3, Hat1, Hpa2, Sas3, and Esa1, which is in contrast to previous conclusions regarding Gcn5. Our findings do reveal that of these HATs, only Gcn5 and Esa1 contribute substantially to gene expression genome wide. Interestingly, histone acetylation at promoter regions throughout the genome does not require TAF1 or RNA polymerase II, indicating that most acetylation is likely to precede transcription and not depend upon it. TAF1 function has been linked to Bdf1, which binds TFIID and acetylated histone H4 tails, but no linkage between TAF1 and the H4 HAT Esa1 has been established. Here, we present evidence for such a linkage through Bdf1.

scholarly journals Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver

2019 ◽  
Author(s):  
Andrew J. Price ◽  
Mohan C. Manjegowda ◽  
Irina M. Bochkis
Keyword(s):  
Gene Expression ◽  
Location Analysis ◽  
Histone Tails ◽  
Post Translational Modifications ◽  
The Core ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Core Histones ◽  
Chromatin Profiling ◽  
Cholesterol Secretion

SummaryPost-translational modifications of histone tails play a crucial role in gene regulation. Here, we performed chromatin profiling by quantitative targeted mass spectrometry to assess all possible modifications of the core histones. We discovered a novel bivalent combination, a dually-marked H3K9me3/H3K14ac modification in the liver, that is significantly decreased in old hepatocytes. Subsequent genome-wide location analysis (ChIP-Seq) identified 1032 and 668 bivalent regions in young and old livers, respectively, with 280 in common. Histone H3K9 deacetylase Hdac3, as well as H3K9 methyltransferase Setdb1, found in complex Kap1, occupied bivalent regions in both young and old livers, correlating to presence of H3K9me3. Expression of genes associated with bivalent regions in young liver, including those regulating cholesterol secretion and triglyceride synthesis, is upregulated in old liver once the bivalency is lost. Hence, H3K9me3/H3K14ac dually-marked regions define a poised inactive state that is resolved with loss of one or both of the chromatin marks, which subsequently leads to change in gene expression.

Genome-Wide DNA Methylation Landscape Defines IGHV Mutated and Unmutated B Cell Chronic Lymphocytic Leukemias

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 526-526
Author(s):  
Junfeng Luo ◽  
Justin Choi ◽  
Lirong Pei ◽  
Farrukh Awan ◽  
Eun-Joon Lee ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
B Cells ◽  
B Cell ◽  
Dna Hypomethylation ◽  
Excellent Correlation ◽  
Methylation Analysis ◽  
Promoter Regions ◽  
Genome Wide ◽  
Dna Methylation Analysis

Abstract Abstract 526 Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. The somatic hypermutation status of the immunoglobulin heavy chain variable (IGHV) genes has been identified as one of the most robust prognostic markers in CLL. Patients with unmutated IGHV status (U-CLL) typically experience an inferior outcome compared to those whose clones express mutated IGHV genes (M-CLL). We conducted a genome-wide DNA methylation analysis in CD19+ B-cells from a group of 43 CLL patients using reduced representation bisulfite sequencing (RRBS). Using base-pair resolution methylation sequencing, 2323 differentially methylated regions between CLL and normal B cells (CLL-specific DMRs) and 569 between M-CLL and U-CLL samples (IGHV-specific DMRs) were identified in the CLL genomes. The IGHV-specific DMRs are mostly unique when compared to the CLL-specific DMRs. Less than 10% of the IGHV-specific DMRs are located in promoter regions; however, more than half of these overlap with known DNase I hypersensitive sites, enhancer regions marked by histone modification (H3K4Me1 and H3K27Ac), and transcription factor binding sites in the ENCODE datasets, which indicates that these DMRs contain regulatory sequences. Distinctive DNA methylation patterns were observed in M-CLL and U-CLL samples. Overall, U-CLL was found to contain 50% more hypermethylated regions than M-CLL samples. The hypermethylated loci observed in the U-CLL samples also appear to be hypermethylated in normal naïve B cells as compared memory B cells, suggesting that M-CLL and U-CLL differ in differentiation status corresponding to normal B cell differentiation stages. RNA-seq analysis performed using matched samples (n=34), in which both DNA methylation and gene expression data were available, demonstrated excellent correlation between DNA methylation and gene expression. Several genes whose expression status was previously shown to be associated with CLL prognosis such as ZAP70, CRY1, LDOC1, SEPT10, LAG3, and LPL were differentially methylated in the promoter regions between M-CLL and U-CLL samples indicating that DNA methylation plays an important role in defining the gene expression patterns of these prognostic genes. We further validated 9 genes with IGHV-specific DMRs in the promoter regions using bisulfite pyrosequencing, and the results demonstrated excellent correlation between differential methylation and IGHV mutation status. These novel differentially methylated genes could be developed into biomarkers for CLL prognosis. In addition, DNA hypomethylation was observed in a significant number of genes involved in lymphocyte activation such as PDCD1, NFATc1, and CD5. DNA hypomethylation was observed in the proximal promoter and far up-stream enhancer regions of CD5, an important cell surface marker that uniquely identifies CLL. Overall, the DNA methylation landscape in CLL patients indicates that CLL B cells possess an active B-cell phenotype; at the same time, U-CLL and M-CLL are faithfully committed to their lineage resembling either naïve or memory B cells. In summary, this comprehensive DNA methylation analysis has identified a large number of novel epigenetic changes in CLL patients. The results from this study will further advance our understanding of the epigenetic contribution to molecular subtypes in CLL. Disclosures: No relevant conflicts of interest to declare.

High-Resolution Genomic Methylation Analysis Using Next Generation Sequencing Identifies Loci Associated With Differential Prognosis In Mantle Cell Lymphoma Patients Treated With Bortezomib + DA-EPOCH-R

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3760-3760
Author(s):  
Violetta V. Leshchenko ◽  
Pei-Yu Kuo ◽  
Deepak Perumal ◽  
Melissa J Fazzari ◽  
Francine E. Garrett-Bakelman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Patient Outcomes ◽  
Next Generation ◽  
Methylation Analysis ◽  
Promoter Regions ◽  
Major Function ◽  
Gene Sets ◽  
Genome Wide ◽  
Cell Growth And Proliferation ◽  
Genomic Methylation

Abstract Forty-three newly diagnosed MCL patients were treated with single agent Bortezomib followed by DA-EPOCH-R (Dunleavy et al, ASH 2012). To understand the genomic and epigenomic basis of differences in patient outcomes, particularly disease free survival (DFS), we carried out high-resolution genome-wide methylation analysis using enhanced RRBS (ERRBS) and correlated cytosine methylation to gene expression (GE) and patient outcomes. For ERRBS, genomic DNA was extracted from CD19+ selected cells from lymph node biopsies or peripheral blood prior to therapy. Library fragment lengths of 150-250 bp and 250-400 bp were prepared and gel isolated per Akalin et al (PLOS Genetics, 2012) and sequencing was performed on an Illumina Hi-seq 2000. 24 out of 24 patient samples passed quality control with methylation assayed at >3.3 million CpG dinucleotides per sample on average 80x coverage per cytosine. Patients were divided into two groups based on 2 year DFS. There were 39,373 differentially methylated (DM) loci (25% difference in methylation, q<0.01) correlating to 3,968 genes between these two groups. The hyper and hypomethylated loci were annotated with hg19 to find gene associations. The annotated analysis represented 74% and 26% hypermethylated loci located in gene body and promoter regions respectively. Similarly, 70% and 30% of hypomethylated loci were located in gene body and promoter regions. Genomic Regions Enrichment of Annotations Tool (GREAT), a next-generation software aimed at the interpretation of genome-wide cis-regulatory data sets, was used to understand the functional significance of identified DM cytosines. Pathway analysis by GREAT for the DM genes showed significant (p<0.05) enrichment for Wnt and Cadherin signaling pathways. 67% of the DM genes had DNA binding transcription factor activity with tumor suppressors BCOR, HIC1, TP73 from hypomethylated genes and oncogenes GATA3 and MAFB from hypermethylated genes. Simultaneously, Cox proportional hazard models evaluating time-to-progression based on RNA expression using Affymetrix U133 Plus 2 arrays identified 1,933 genes as significantly (p<0.05) associated with DFS. The top canonical pathways enriched by these genes included Protein Kinase A Signaling, PI3K/AKT Signaling, and Protein Ubiquitination Pathway. Top molecular functions of prognostic loci by GEP were cell growth and proliferation. Our analysis has shown that high expression of CDC25A, NFKB2, GLI3, FOXO3, and USP9X were likely associated with increased hazard risk in MCL patient after Bortezomib + DA-EPOCH-R treatment. The gene sets identified by the two platforms were distinct, with only 343 genes in common between DM and DE genes. Based on these findings, we conclude that genomic methylation analysis by next-generation sequencing can identify functionally important cis-regulatory cytosines associated with prognosis in MCL. Prognostic gene sets identified by methylation and gene expression were distinct with transcriptional regulation being the major function of DM genes while cell growth and proliferation being the major function of DE genes. We are developing an integrated prognostic platform for patient outcomes following Bortezomib + DA-EPOCH-R combining genomic methylation and gene expression. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Analysis of Glucosinolate Content and Metabolism Related Genes in Different Parts of Chinese Flowering Cabbage

2022 ◽  
Vol 12 ◽  
Author(s):  
Xianjun Feng ◽  
Jiajun Ma ◽  
Zhiqian Liu ◽  
Xuan Li ◽  
Yinghua Wu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Glucosinolate Content ◽  
Vegetable Crops ◽  
Flower Buds ◽  
Flower Bud ◽  
Expression Of Genes ◽  
Genes Encoding ◽  
Cruciferous Plants ◽  
Risk Of Cancer ◽  
Different Parts

Glucosinolates (GSLs) are important secondary metabolites that play important defensive roles in cruciferous plants. Chinese flowering cabbage, one of the most common vegetable crops, is rich in GSLs and thus has the potential to reduce the risk of cancer in humans. Many genes that are involved in GSL biosynthesis and metabolism have been identified in the model plant Arabidopsis thaliana; however, few studies investigated the genes related to GSL biosynthesis and metabolism in Chinese flowering cabbage. In the present study, the GSL composition and content in three different organs of Chinese flowering cabbage (leaf, stalk, and flower bud) were determined. Our results showed that the total GSL content in flower buds was significantly higher than in stalks and leaves, and aliphatic GSLs were the most abundant GSL type. To understand the molecular mechanisms underlying the variations of GSL content, we analyzed the expression of genes encoding enzymes involved in GSL biosynthesis and transport in different tissues of Chinese flowering cabbage using RNA sequencing; the expression levels of most genes were found to be consistent with the pattern of total GSL content. Correlation and consistency analysis of differentially expressed genes from different organs with the GSL content revealed that seven genes (Bra029966, Bra012640, Bra016787, Bra011761, Bra006830, Bra011759, and Bra029248) were positively correlated with GSL content. These findings provide a molecular basis for further elucidating GSL biosynthesis and transport in Chinese flowering cabbage.

scholarly journals Fatty Acid and Transcript Profiling in Developing Seeds of Three Brassica napus Cultivars

2015 ◽  
Vol 72 (1) ◽  
pp. 3-32
Author(s):  
Mariana Petkova ◽  
Wun S. Chao ◽  
Leonard Cook ◽  
Mark West ◽  
Mukhlesur Rahman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Brassica Napus ◽  
Erucic Acid ◽  
Seed Development ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Eicosenoic Acid ◽  
Expression Of Genes ◽  
Spring Canola

Abstract Fatty acid levels and gene expression profiles for selected genes associated with the synthesis of fatty acids (FA), triacylglycerol, and oil body proteins were examined in three oilseed rape (Brassica napus) cultivars that have utility for cultivar development in our spring canola breeding program. The seed oil content of Bronowski, Q2, and Westar was 39.0, 40.1, and 40.6%, respectively at 40 days after flowering (DAF). During the 20 to 40 day period of seed development, cultivars had varying levels of palmitic, stearic, oleic, linoleic, α-linolenic, eicosenoic, and erucic acid. In general, the percentage of each FA was similar among the cultivars during seed development. However, the level of oleic acid was lower and the levels of eicosenoic acid and erucic acid were higher in Bronowski than in Q2 and Westar seeds; linoleic acid also tended to be lower in Bronowski. Gene expression among the cultivars was similar from 10 to 40 DAF. The few exceptions were that expression of KAS1 and SAD were higher in Westar and Q2 than in Bronowski at 25 DAF, SAD was highest in Q2, intermediate in Westar, and lowest in Bronowski at 35 DAF, FAD2 was higher in Q2 than in Bronowski at 35 DAF, FAD3 was higher in Q2 than in Bronowski at 15 DAF and Q2 and Westar at 25 and 30 DAF, and FAE1 was higher in Westar and Q2 than in Bronowski at 30 DAF. Correlation analysis for gene expression against DAF for each genotype supported a common trend in gene expression among the three cultivars with gene expression tending to decrease over time; except for LPAAT, which tended to increase. The correlation between the level of FAs and expression of genes by genotype indicated no general trend; rather correlations seem to depend on the genotype.

scholarly journals Gene expression of settled and metamorphosed Orbicella faveolata during establishment of symbiosis

2017 ◽  
Author(s):  
Aubrie O'Rourke ◽  
Aki Ohdera ◽  
Shinichi Sunagawa ◽  
Erika M Diaz-Almeyda ◽  
Michael K DeSalvo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nutrient Metabolism ◽  
Transcriptomic Response ◽  
Tropical Oceans ◽  
Expression Of Genes ◽  
Expression Studies ◽  
Genome Wide ◽  
Orbicella Faveolata ◽  
Algal Symbiosis ◽  
Differential Gene

Corals rely on a symbiosis with dinoflagellate algae (Symbiodinium spp.) to thrive in nutrient poor tropical oceans. However, the coral-algal symbiosis can break down during bleaching events, potentially leading to coral death. While genome-wide expression studies have shown the genes associated with the breakdown of this partnership, the full conglomerate of genes responsible for the establishment and maintenance of a healthy symbiosis remains unknown. Results from previous studies suggested little transcriptomic change associated with the establishment of symbiosis. We examined the transcriptomic response of the coral Orbicella faveolata in the presence (symbiotic) and absence (aposymbiotic) of Symbiodinium minutum, one of its associated symbionts. 9 days post-metamorphic aposymbiotic coral polyps of O. faveolata were compared to symbiotic coral polyps and the subsequent differential gene expression between control and treatment was quantified using cDNA microarray technology. Coral polyps exhibited differential expression of genes associated with nutrient metabolism and development, providing insight into control of pathways as a result of symbiosis driving early polyp growth. Furthermore, genes associated with lysosomal fusion were also upregulated, suggesting host regulation of symbiont densities soon after infection.

scholarly journals Meta-Analysis of RNA-Seq Studies Reveals Genes With Dominant Functions During Flower Bud Endo- To Eco-Dormancy Transition in Prunus Species

2021 ◽  
Author(s):  
Monica Canton ◽  
Cristian Forestan ◽  
Claudio Bonghi ◽  
Serena Varotto
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Fruit Trees ◽  
Day Length ◽  
Specific Gene ◽  
Flower Buds ◽  
Flower Bud

Abstract In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. Each species and/or cultivar requires exposure to low winter temperature followed by warm temperatures, quantified as chilling and heat requirements, to remove the physiological blocks that inhibit budburst. A comprehensive meta-analysis of transcriptomic studies on flower buds of sweet cherry, apricot and peach was conducted, by investigating the gene expression profiles during bud endo- to ecodormancy transition in genotypes differing in chilling requirements. Conserved and distinctive expression patterns were observed, allowing the identification of gene specifically associated with endodormancy or ecodormancy. In addition to the MADS-box transcription factor family, hormone-related genes, chromatin modifiers, macro- and micro-gametogenesis related genes and environmental integrators, were identified as novel biomarker candidates for flower bud development during winter in stone fruits. In parallel, flower bud differentiation processes were associated to dormancy progression and termination and to environmental factors triggering dormancy phase-specific gene expression.

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