scholarly journals Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

2021 ◽  
Author(s):  
Sergio Alan Cervantes-Pérez ◽  
Lenin Yong-Villalobos ◽  
Nathalia M.V. Florez-Zapata ◽  
Araceli Oropeza-Aburto ◽  
Felix Rico-Reséndiz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genome Size ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Initial Step ◽  
Global Dna Methylation ◽  
Small Interfering Rnas ◽  
Utricularia Gibba ◽  
The Impact ◽  
Female Gametogenesis

Abstract The most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in compact plant genomes. Because the small genome size of the carnivorous plant Utricularia gibba we investigate the noncoding RNA landscape and global DNA methylation in a compact genome. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of noncoding RNAs and reduced global DNA methylation levels, as determined by a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, reduced DNA methylation correlates with lack of a functional RdDM pathway, as U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs lost key domains required for complete function. Our findings unveil that lack of a functional DCL3 in U. gibba correlates with a decreased proportion of 24-nt small-interfering RNAs, low genome methylation levels, and developmental abnormalities during female gametogenesis that are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of apomixis in compact genomes.

scholarly journals Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sergio Alan Cervantes-Pérez ◽  
Lenin Yong-Villalobos ◽  
Nathalia M. V. Florez-Zapata ◽  
Araceli Oropeza-Aburto ◽  
Félix Rico-Reséndiz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Initial Step ◽  
Carnivorous Plant ◽  
Small Interfering Rnas ◽  
Developmental Abnormalities ◽  
Utricularia Gibba ◽  
The Impact ◽  
Female Gametogenesis

AbstractThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), a conserved mechanism that involves the role of noncoding RNAs to control the expansion of the noncoding genome. Genome-wide DNA methylation levels have been reported to correlate with genome size. However, little is known about the catalog of noncoding RNAs and the impact on DNA methylation in small plant genomes with reduced noncoding regions. Because of the small length of intergenic regions in the compact genome of the carnivorous plant Utricularia gibba, we investigated its repertoire of noncoding RNA and DNA methylation landscape. Here, we report that, compared to other angiosperms, U. gibba has an unusual distribution of small RNAs and reduced global DNA methylation levels. DNA methylation was determined using a novel strategy based on long-read DNA sequencing with the Pacific Bioscience platform and confirmed by whole-genome bisulfite sequencing. Moreover, some key genes involved in the RdDM pathway may not represented by compensatory paralogs or comprise truncated proteins, for example, U. gibba DICER-LIKE 3 (DCL3), encoding a DICER endonuclease that produces 24-nt small-interfering RNAs, has lost key domains required for complete function. Our results unveil that a truncated DCL3 correlates with a decreased proportion of 24-nt small-interfering RNAs, low DNA methylation levels, and developmental abnormalities during female gametogenesis in U. gibba. Alterations in female gametogenesis are reminiscent of RdDM mutant phenotypes in Arabidopsis thaliana. It would be interesting to further study the biological implications of the DCL3 truncation in U. gibba, as it could represent an initial step in the evolution of RdDM pathway in compact genomes.

scholarly journals Atypical DNA methylation, sRNA size distribution and female gametogenesis correlate with genome compaction in Utricularia gibba

2020 ◽  
Author(s):  
Sergio Alan Cervantes-Pérez ◽  
Lenin Yong-Villalobos ◽  
Nathalia M. V. Florez-Zapata ◽  
Araceli Oropeza-Aburto ◽  
Félix Rico-Reséndiz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genome Size ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Initial Step ◽  
Carnivorous Plant ◽  
Plant Genome ◽  
List Type ◽  
Utricularia Gibba

SummaryThe most studied DNA methylation pathway in plants is the RNA Directed DNA Methylation (RdDM), which is a conserved mechanism that involves noncoding-RNAs to control the expansion of intergenic regions. However, little is known about relationship between plant genome size reductions and DNA methylation.Because the compact genome size of the carnivorous plant Utricularia gibba, we investigate in this plant the noncoding-RNA landscape and DNA methylation through a combination of cytological, evolutionary, and genome-wide transcriptomic and methylation approaches.We report an unusual distribution of noncoding RNAs in U. gibba in comparison with other characterized angiosperms, which correlated with a lower level of global genome methylation, as determined by a novel strategy based on long-read DNA sequencing and corroborated by whole-genome bisulfite analysis. Moreover, found that genes involved in the RdDM pathway may not be functionally active in U. gibba, including a truncated DICER-LIKE 3 (DCL3), involved in the production of 24-nt small-RNAs.Our findings suggest that selective pressure to conserve a fully functional RdDM pathway might be reduced in compact genomes and a defective DCL3 correlate with a decreased proportion of 24-nt small-RNAs and developmental alterations in U. gibba, which could represent an initial step in the evolution of apomixis.

scholarly journals The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice

2021 ◽  
Vol 118 (30) ◽  
pp. e2100709118
Author(s):  
Kezhi Zheng ◽  
Lili Wang ◽  
Longjun Zeng ◽  
Dachao Xu ◽  
Zhongxin Guo ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Rna Polymerase ◽  
Histone Modifications ◽  
Noncoding Rna ◽  
De Novo ◽  
Noncoding Rnas ◽  
Reproductive Development ◽  
Small Interfering Rnas ◽  
Pol V ◽  
Specific Manner

RNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of RNA polymerase V (Pol V), a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long noncoding RNAs. Pol V influences the accumulation of 24-nucleotide small interfering RNAs (24-nt siRNAs) in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high CHH methylation levels and low CG and CHG methylation levels tends to depend on Pol V. In contrast, low methylation levels in the CHH context and high methylation levels in CG and CHG contexts predisposes 24-nt siRNA accumulation to be independent of Pol V. H3K9me1 and H3K9me2 tend to be enriched on Pol V–independent 24-nt siRNA loci, whereas various active histone modifications are enriched on Pol V–dependent 24-nt siRNA loci. DNA methylation is required for 24-nt siRNAs biosynthesis on Pol V–dependent loci but not on Pol V–independent loci. Our results reveal the function of rice Pol V for long noncoding RNA production, DNA methylation, 24-nt siRNA accumulation, and reproductive development.

scholarly journals Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications

2019 ◽  
Vol 20 (14) ◽  
pp. 3478 ◽  
Author(s):  
Michal J. Dabrowski ◽  
Bartosz Wojtas
Keyword(s):  
Dna Methylation ◽  
Histone Modifications ◽  
Global Gene Expression ◽  
Global Dna Methylation ◽  
Epigenetic Changes ◽  
Human Gliomas ◽  
Human Pathology ◽  
Different Types ◽  
Methylation Patterns ◽  
The Impact

During the last two decades, several international consortia have been established to unveil the molecular background of human cancers including gliomas. As a result, a huge outbreak of new genetic and epigenetic data appeared. It was not only shown that gliomas share some specific DNA sequence aberrations, but they also present common alterations of chromatin. Many researchers have reported specific epigenetic features, such as DNA methylation and histone modifications being involved in tumor pathobiology. Unlike mutations in DNA, epigenetic changes are more global in nature. Moreover, many studies have shown an interplay between different types of epigenetic changes. Alterations in DNA methylation in gliomas are one of the best described epigenetic changes underlying human pathology. In the following work, we present the state of knowledge about global DNA methylation patterns in gliomas and their interplay with histone modifications that may affect transcription factor binding, global gene expression and chromatin conformation. Apart from summarizing the impact of global DNA methylation on glioma pathobiology, we provide an extract of key mechanisms of DNA methylation machinery.

scholarly journals Could the Epigenetics of Eosinophils in Asthma and Allergy Solve Parts of the Puzzle?

2021 ◽  
Vol 22 (16) ◽  
pp. 8921
Author(s):  
Émile Bélanger ◽  
Catherine Laprise
Keyword(s):  
Dna Methylation ◽  
Social Factors ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Allergic Diseases ◽  
Epigenetic Mechanisms ◽  
Cell Type ◽  
Asthma And Allergy ◽  
Allergies And Asthma

Epigenetics is a field of study investigating changes in gene expression that do not alter the DNA sequence. These changes are often influenced by environmental or social factors and are reversible. Epigenetic mechanisms include DNA methylation, histone modification, and noncoding RNA. Understanding the role of these epigenetic mechanisms in human diseases provides useful information with regard to disease severity and development. Several studies have searched for the epigenetic mechanisms that regulate allergies and asthma; however, only few studies have used samples of eosinophil, a proinflammatory cell type known to be largely recruited during allergic or asthmatic inflammation. Such studies would enable us to better understand the factors that influence the massive recruitment of eosinophils during allergic and asthmatic symptoms. In this review, we sought to summarize different studies that aimed to discover differential patterns of histone modifications, DNA methylation, and noncoding RNAs in eosinophil samples of individuals with certain diseases, with a particular focus on those with asthma or allergic diseases.

Dysregulation of DNA Methylation Involves in Progression of Myeloid Leukemia in Down Syndrome

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 89-89 ◽  
Author(s):  
Satoshi Saida ◽  
Masahiro Nakamura ◽  
Tsutomu Toki ◽  
Yoko Nishinaka-Arai ◽  
Kiminori Terui ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Down Syndrome ◽  
First Generation ◽  
Xenograft Model ◽  
Methylation Profile ◽  
Clinical Samples ◽  
Global Dna Methylation ◽  
Dna Methylation Profile ◽  
Malignant Conversion ◽  
The Impact

Abstract Transient abnormal myelopoiesis (TAM) is a clonal pre-leukemic disorder in neonates of Down syndrome. Although self-limiting in a majority of cases, TAM may evolve as non-self-limiting acute megakaryoblastic leukemia (DS-AMKL) after spontaneous remission. As such, the study of TAM/DS-AMKL can provide insight into the mechanisms of leukemic evolution. Our recent study has shown that DS-AMKL from TAM is shaped by acquisition of new mutations and clonal selection, and genomic mutations in epigenetic regulators frequently preceded other driver mutations. In this study, we address biological significance of the mutations in a progression from TAM to DS-AMKL using a newly established xenograft model of malignant conversion of the leukemia. We first analyzed global DNA methylation profile of clinical samples including 21 TAM and 10 DS-AMKL, using Infiniun 450K DNA methylation array (Illumina). Although averaged DNA methylation levels of both TAM and DS-AMKL were approximately the same, we observed two distinct clusters delineating TAM and DS-AMKL samples by both hierarchical clustering and principle component analysis (PCA). We identified differentially methylated cytosines on the promoters (TAM/AMKL-DMCpGs) between the two groups, and found that most of TAM/AMKL-DMCpGs were hyper-methylated in DS-AMKL samples compared to TAM, indicating that hyper-methylation of the subset of CpGs is a hallmark of DS-AMKL. To follow sequential alterations of DNA methylation profile, we established a xenograft model of the leukemia, which mimicked the progression of TAM to DS-AMKL. We transplanted TAM blast cells (1x106 cells) derived from the patient, who developed DS-AMKL later, into NOD/SCID/γc null (NOG) mice through tail vein. One series of the xenografts exhibited engraftment in the mouse and could passage by serial engraftment in vivo, whereas the other exhibited engraftment, but could not maintain in the mice by serial transplantation. The global DNA methylation profile of engrafted cells from the first generation mice was closed to TAM patients, whereas those from the forth, fifth and sixth generations approached to DS-AMKL patients. Moreover, hyper-methylation of TAM/AMKL-DMCpGs was also observed in engrafted TAM cells with higher numbers of passages, demonstrated that the xenograft model mimicked dysregulation of DNA methylation in disease progression of TAM. We further investigated the impact of dysregulation of DNA methylation on gene expression. As expected, RNA-seq and hierarchal clustering analyses of genes regulated by TAM/AMKL-DMCpGs displayed distinct two clusters, one with TAM samples and the first generation engraftments and another with DS-AMKL samples and 4th, 5th and 6th generation engraftments. We propose that epigenetic dysregulation is a crucial step for malignant conversion of TAM into DS-AMKL. Disclosures No relevant conflicts of interest to declare.

scholarly journals Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa and related species

2020 ◽  
Author(s):  
Hasan Mehraj ◽  
Daniel J. Shea ◽  
Satoshi Takahashi ◽  
Naomi Miyaji ◽  
Ayasha Akter ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Small Interfering Rnas ◽  
Genome Wide ◽  
Rna Fragments ◽  
Aa Genome ◽  
Seed Crops ◽  
Genomic Regions

AbstractLong noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression were analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels and when both were present, there were further increase in DNA methylation levels. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. Brassica rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events, but the detailed mechanism is not known. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of the B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and offers insights into the function of lncRNA in the Brassica genus.

scholarly journals Methionine Supply During Late-Gestation Triggers Offspring Sex-Specific Divergent Changes in Metabolic and Epigenetic Signatures in Bovine Placenta

2019 ◽  
Vol 149 (1) ◽  
pp. 6-17 ◽  
Author(s):  
Fernanda Batistel ◽  
Abdulrahman S Alharthi ◽  
Rainie R C Yambao ◽  
Ahmed A Elolimy ◽  
Yuan-Xiang Pan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Body Mass ◽  
Carbon Metabolism ◽  
Control Diet ◽  
Late Gestation ◽  
Global Dna Methylation ◽  
Similar Data ◽  
Offspring Sex ◽  
One Carbon Metabolism ◽  
The Impact

ABSTRACT Background Nonruminant male and female offspring respond differently to gestational nutrition, with placenta contributing to the underlying mechanisms. However, similar data are lacking in large ruminants. Objectives The aim of this study was to investigate the impact of methionine supply during late-gestation on metabolism and DNA methylation in placenta from cows carrying male or female calves. Methods During the last 28 d of pregnancy, cows were individually fed a control diet (CON) or the control diet plus rumen-protected d,l-methionine (MET; 0.9 g/kg dry matter intake). Placentomes collected at term were classified according to cow dietary treatment and offspring sex as follows: Male CON (n = 7), Male MET (n = 7), Female CON (n = 8), and Female MET (n = 8). Calf growth was measured until 9 wk of age. Targeted metabolomics, RT-PCR, global DNA methylation, and activity of selected enzymes in one-carbon metabolism and transsulfuration pathways were performed. Statistics were conducted via ANOVA using MIXED models. Results At birth, Male MET calves were heavier than Male CON calves (7.6%, P = 0.02), but body mass was similar at 9 wk of age. In contrast, compared with Female CON, Female MET calves had greater body mass at 9 wk of age (6.3%, P = 0.03). Compared with Male CON, placenta from Male MET calves had greater concentrations of tricarboxylic acid (TCA) cycle and transsulfuration intermediates (23–100%, P < 0.05), along with greater 5-methyltetrahydrofolatehomocysteine methyltransferase activity (67%, P = 0.03). Compared with Female CON, placenta from Female MET calves had greater concentrations of one-carbon metabolism intermediates (13–52%, P < 0.05). DNA methyltransferase 3A (DNMT3A) was upregulated (43%, P < 0.01) in placenta from Female MET compared with Female CON calves. Global DNA methylation was lower in placenta from Female MET compared with Female CON calves (45%, P = 0.06). Conclusions Methionine supply affects placental metabolism, DNA methylation, and body mass of the calf in a sex-specific manner, underscoring its importance as dietary methyl-donor for pregnant cows.

scholarly journals Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0242530
Author(s):  
Hasan Mehraj ◽  
Daniel J. Shea ◽  
Satoshi Takahashi ◽  
Naomi Miyaji ◽  
Ayasha Akter ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Small Interfering Rnas ◽  
Genome Wide ◽  
Rna Fragments ◽  
Aa Genome ◽  
Seed Crops ◽  
Genomic Regions

Long noncoding RNAs (lncRNAs) are RNA fragments that generally do not code for a protein but are involved in epigenetic gene regulation. In this study, lncRNAs of Brassica rapa were classified into long intergenic noncoding RNAs, natural antisense RNAs, and intronic noncoding RNAs and their expression analyzed in relation to genome-wide 24-nt small interfering RNAs (siRNAs), DNA methylation, and histone H3 lysine 27 trimethylation marks (H3K27me3). More than 65% of the lncRNAs analyzed consisted of one exon, and more than 55% overlapped with inverted repeat regions (IRRs). Overlap of lncRNAs with IRRs or genomic regions encoding for 24-nt siRNAs resulted in increased DNA methylation levels when both were present. LncRNA did not overlap greatly with H3K27me3 marks, but the expression level of intronic noncoding RNAs that did coincide with H3K27me3 marks was higher than without H3K27me3 marks. The Brassica genus comprises important vegetables and oil seed crops grown across the world. B. rapa is a diploid (AA genome) thought to be one of the ancestral species of both B. juncea (AABB genome) and B. napus (AACC) through genome merging (allotetrapolyploidization). Complex genome restructuring and epigenetic alterations are thought to be involved in these allotetrapolyploidization events. Comparison of lncRNAs between B. rapa and B. nigra, B. oleracea, B. juncea, and B. napus showed the highest conservation with B. oleracea. This study presents a comprehensive analysis of the epigenome structure of B. rapa at multi-epigenetic levels (siRNAs, DNA methylation, H3K27me3, and lncRNAs) and identified a suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus.

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