scholarly journals Seed Genome Hypomethylated Regions Are Enriched In Transcription Factor Genes

2018 ◽  
Author(s):  
Min Chen ◽  
Jer-Young Lin ◽  
Jungim Hur ◽  
Julie M. Pelletier ◽  
Russell Baden ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Seed Development ◽  
Mammalian Cells ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Storage Proteins ◽  
Seed Formation ◽  
Epigenetic Events ◽  
Transcription Factor Genes

AbstractThe precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators, such as ABI3 and FUS3, are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes, and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from post-fertilization through dormancy and germination for regions that contain < 5% or < 0.4% bulk methylation in CG-, CHG-, and CHH-contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5 to 76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor genes, and other developmental genes, that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue - and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development - probably by the action of specific transcription factors and epigenetic events at the chromatin level.SignificanceWe scanned soybean and Arabidopsis seed genomes for hypomethylated regions, or DNA Methylation Valleys (DMVs), present in mammalian cells. A significant fraction of seed genomes contain DMV regions that have < 5% bulk DNA methylation, or, in many cases, no detectable DNA methylation. Methylation levels of seed DMVs do not vary detectably during seed development with respect to time, region, and tissue, and are present prior to fertilization. Seed DMVs are enriched in transcription factor genes and other genes critical for seed development, and are also decorated with histone marks that fluctuate with developmental stage, resembling in significant ways their animal counterparts. We conclude that many genes playing important roles in seed formation are regulated in the absence of detectable DNA methylation events, and suggest that selective action of transcriptional activators and repressors, as well as chromatin epigenetic events play important roles in making a seed - particularly embryo formation.

scholarly journals Seed genome hypomethylated regions are enriched in transcription factor genes

2018 ◽  
Vol 115 (35) ◽  
pp. E8315-E8322 ◽  
Author(s):  
Min Chen ◽  
Jer-Young Lin ◽  
Jungim Hur ◽  
Julie M. Pelletier ◽  
Russell Baden ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Seed Development ◽  
Mammalian Cells ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Storage Proteins ◽  
Seed Formation ◽  
Epigenetic Events ◽  
Transcription Factor Genes ◽  
Plant Life Cycle

The precise mechanisms that control gene activity during seed development remain largely unknown. Previously, we showed that several genes essential for seed development, including those encoding storage proteins, fatty acid biosynthesis enzymes, and transcriptional regulators (e.g., ABI3, FUS3) are located within hypomethylated regions of the soybean genome. These hypomethylated regions are similar to the DNA methylation valleys (DMVs), or canyons, found in mammalian cells. Here, we address the question of the extent to which DMVs are present within seed genomes and what role they might play in seed development. We scanned soybean and Arabidopsis seed genomes from postfertilization through dormancy and germination for regions that contain <5% or <0.4% bulk methylation in CG, CHG, and CHH contexts over all developmental stages. We found that DMVs represent extensive portions of seed genomes, range in size from 5–76 kb, are scattered throughout all chromosomes, and are hypomethylated throughout the plant life cycle. Significantly, DMVs are enriched greatly in transcription factor (TF) genes and other developmental genes that play critical roles in seed formation. Many DMV genes are regulated with respect to seed stage, region, and tissue, and contain H3K4me3, H3K27me3, or bivalent marks that fluctuate during development. Our results indicate that DMVs are a unique regulatory feature of both plant and animal genomes, and that a large number of seed genes are regulated in the absence of methylation changes during development, probably by the action of specific TFs and epigenetic events at the chromatin level.

DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides)

2019 ◽  
Vol 46 (2) ◽  
pp. 152 ◽  
Author(s):  
Aleksandra M. Staszak ◽  
Monika Rewers ◽  
Elwira Sliwinska ◽  
Ewelina A. Klupczynska ◽  
Tomasz A. Pawlowski
Keyword(s):  
Seed Development ◽  
Dna Content ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Protein A ◽  
Embryo Axis ◽  
Norway Maple ◽  
Physiological Dormancy ◽  
Antioxidant Proteins ◽  
Mature Seeds

Mature seeds of Norway maple exhibit desiccation tolerance and deep physiological dormancy. Flow cytometry, proteomics, and immunodetection have been combined to investigate seed development of this species. DNA content analysis revealed that cell cycle/endoreduplication activity differs between seed organs and developmental stages. In the embryo axis, the proportion of the nuclei with the highest DNA content (4C) increases at the beginning of maturation (17 weeks after flowering; WAF), and then is stable until the end of maturation, to increase again after drying. In cotyledons, during maturation endopolyploid nuclei (8C) occur and the intensity of endoreduplication increases up to 21 WAF, and then is stable until development is completed. In dry mature seeds, the proportion of 4C nuclei is high, and reaches 36% in the embryo axis and 52% in cotyledons. Proteomic studies revealed that energy and carbon metabolism, fatty acid biosynthesis, storage and antioxidant proteins are associated with seed development. Study of the ABI5 protein, a transcription factor involved in ABA signalling, and the RGL2 protein, a repressor of the GA signalling indicates that the highest accumulation of these proteins occurs in fully-matured and dried seeds. It is suggested that this increase in accumulation can be associated with completion of maturation, mainly with desiccation and dormancy acquisition.

scholarly journals The Dynamic Changes of DNA Methylation and Histone Modifications of Salt Responsive Transcription Factor Genes in Soybean

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41274 ◽  
Author(s):  
Yuguang Song ◽  
Dandan Ji ◽  
Shuo Li ◽  
Peng Wang ◽  
Qiang Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Histone Modifications ◽  
Dynamic Changes ◽  
Transcription Factor Genes

scholarly journals The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

2019 ◽  
Author(s):  
Yunduan Li ◽  
Songlin Zhang ◽  
Ruzhuang Dong ◽  
Li Wang ◽  
Jin Yao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Signaling Pathways ◽  
Seed Development ◽  
Cytosine Methylation ◽  
Fruit Size ◽  
Homeobox Gene ◽  
Seed Number ◽  
Homeodomain Transcription Factors

Abstract Background: The homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported. Results: Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion. Conclusion: VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

scholarly journals The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yunduan Li ◽  
Songlin Zhang ◽  
Ruzhuang Dong ◽  
Li Wang ◽  
Jin Yao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Signaling Pathways ◽  
Seed Development ◽  
Cytosine Methylation ◽  
Fruit Size ◽  
Homeobox Gene ◽  
Seed Number ◽  
Homeodomain Transcription Factors

Abstract Background The homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported. Results Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion. Conclusion VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

scholarly journals Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development

2017 ◽  
Vol 114 (45) ◽  
pp. E9730-E9739 ◽  
Author(s):  
Jer-Young Lin ◽  
Brandon H. Le ◽  
Min Chen ◽  
Kelli F. Henry ◽  
Jungim Hur ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Seed Development ◽  
Significant Role ◽  
Regulatory Networks ◽  
Storage Proteins ◽  
Seed Proteins ◽  
Regulatory Elements ◽  
Genetic Regulatory Networks ◽  
Global Changes ◽  
Seed Formation

We profiled soybean and Arabidopsis methylomes from the globular stage through dormancy and germination to understand the role of methylation in seed formation. CHH methylation increases significantly during development throughout the entire seed, targets primarily transposable elements (TEs), is maintained during endoreduplication, and drops precipitously within the germinating seedling. By contrast, no significant global changes in CG- and CHG-context methylation occur during the same developmental period. An Arabidopsis ddcc mutant lacking CHH and CHG methylation does not affect seed development, germination, or major patterns of gene expression, implying that CHH and CHG methylation does not play a significant role in seed development or in regulating seed gene activity. By contrast, over 100 TEs are transcriptionally de-repressed in ddcc seeds, suggesting that the increase in CHH-context methylation may be a failsafe mechanism to reinforce transposon silencing. Many genes encoding important classes of seed proteins, such as storage proteins, oil biosynthesis enzymes, and transcription factors, reside in genomic regions devoid of methylation at any stage of seed development. Many other genes in these classes have similar methylation patterns, whether the genes are active or repressed. Our results suggest that methylation does not play a significant role in regulating large numbers of genes important for programming seed development in both soybean and Arabidopsis. We conclude that understanding the mechanisms controlling seed development will require determining how cis-regulatory elements and their cognate transcription factors are organized in genetic regulatory networks.

scholarly journals Identification of Novel Candidate Genes Implicated in Odontogenic Potential in the Developing Mouse Tooth Germ using Transcriptome Analysis

2021 ◽  
Author(s):  
Yeo-Kyeong Shin ◽  
Seongmin Cheon ◽  
Sung-Duk Kim ◽  
Jung-Sun Moon ◽  
Jae-Young Kim ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Developmental Stages ◽  
Tooth Development ◽  
Tooth Germ ◽  
Molar Tooth ◽  
Gene Enhancer ◽  
Transcription Factor Genes ◽  
Homeobox Protein ◽  
New Perspective ◽  
Whole Transcriptome

Abstract In tooth bioengineering for replacement therapy of missing teeth, the utilized cells must possess an inductive signal-forming ability to initiate odontogenesis. This ability is called odontogenic potential. In mice, the odontogenic potential signal is known to be translocated from the epithelium to the mesenchyme at the early bud stage in the developing molar tooth germ. However, the identity of the molecular constituents of this process remains unclear. Therefore, in this study, whole transcriptome profiles of the mouse molar tooth germ epithelium and mesenchyme were investigated using the RNA sequencing (RNA-seq) technique. The analyzed transcriptomes corresponded to two developmental stages, embryonic day 11.5 (E11.5) and 14.5 (E14.5), which represent the odontogenic potential shifts. We identified differentially expressed genes (DEGs), which were specifically overexpressed in both the E11.5 epithelium and E14.5 mesenchyme, but not expressed in their respective counterparts. Of the fifty-five DEGs identified, the top three most expressed transcription factor genes (transcription factor AP-2 beta isoform 3 [TFAP2B], developing brain homeobox protein 2 [DBX2], and insulin gene enhancer protein ISL-1 [ISL1]) and three tooth development-related genes (transcription factor HES-5 [HES5], platelet-derived growth factor D precursor [PDGFD], semaphrin-3A precursor [SEMA3A]) were selected and validated by quantitative RT-PCR. Using immunofluorescence staining, the TFAP2B protein expression was found to be localized only at the E11.5 epithelium and E14.5 mesenchyme. Thus, our empirical findings in the present study may provide a new perspective into the characterization of the molecules responsible for the odontogenic potential and may have an implication in the cell-based whole tooth regeneration strategy.

scholarly journals The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

2019 ◽  
Author(s):  
Yunduan Li ◽  
Songlin Zhang ◽  
Ruzhuang Dong ◽  
Li Wang ◽  
Jin Yao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Signaling Pathways ◽  
Seed Development ◽  
Cytosine Methylation ◽  
Fruit Size ◽  
Homeobox Gene ◽  
Seed Number ◽  
Homeodomain Transcription Factors

Abstract Background: The homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported.Results: Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion.Conclusion: VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

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