scholarly journals Response of wheat DREB transcription factor to drought stress based on DNA methylation

2021 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Expression Patterns ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought, dehydration responsive element binding protein (DREB) plays an important role in the response of plant to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat AK58, and one 712-bp intron was identified in DREB6. Although AP2/EREBP domains of DREB2, DREB6 and Wdreb2 showed 73.25% identity, they belong to different types of DREB transcription factor. Under drought stress, different transcript expression patterns of DREB2, DREB6 and Wdreb2 were observed, and their expression had tissue specificity, was obviously higher in leaves. Promoters of DREB2, DREB6 and Wdreb2 were further studied, some elements related to stresses were found, and the promoters of DREB2 and Wdreb2 were slightly methylated, but DREB6 promoter was moderately methylated. Compared with the control, the level of promoter methylation in DREB2 and DREB6 decreased after 2 h stress treatment, and then increased, which was opposite in Wdreb2 promoter, the status of promoter methylation in DREB2, DREB6 and Wdreb2 also had significant changes under drought stress. Further analysis showed that promoter methylation of DREB6 and Wdreb2 was negatively correlated with their expression, especially in Wdreb2. Conclusions: Our data suggest the different functions of DREB2, DREB6 and Wdreb2 in response to drought stress, and demonstrate the strong effects of promoter methylation on the regulation of Wdreb2 and DREB6 gene expression.

scholarly journals Response of DREB transcription factor to drought stress based on DNA methylation in wheat

2020 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Resistance Mechanism ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought stress, and the research on drought resistance mechanism of wheat is very important. Dehydration responsive element binding protein (DREB) plays an important role in plant response to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat in this study, their CDS sequence was composed of 732bp, 837bp or 1035bp, respectively, one 712bp intron was found in DREB6. Although AP2/EREBP domain of DREB2, DREB6 and Wdreb2 had 73.25% identity, they belong to different types of DREB transcription factor, and the expression of Wdreb2 was significantly higher, yet was the lowest in DREB2. Under drought stress, the expression of DREB2, DREB6 and Wdreb2 could be induced, but had different trends along with the increase of stress time, and their expression had tissue specificity, was obviously higher in leaf. Promoter of DREB2, DREB6 and Wdreb2 in leaf was further studied, some elements related to adverse stress were found, and the promoter of DREB2 and Wdreb2 was slightly methylated, but DREB6 promoter was mildly methylated. Compared with the control, the level of promoter methylation decreased in DREB2 and DREB6 as stressed for 2h, then increased along with the increase of stress time, which was opposite in Wdreb2 promoter, the status of promoter methylation also had significant change under drought stress. Further analysis showed that promoter methylation of DREB6 or Wdreb2 was negatively correlated with their expression, especially was significant in Wdreb2. Conclusions: DREB2, DREB6 and Wdreb2 might function differently in response to drought stress, and promoter methylation had more significant effects on gene expression of Wdreb2 and DREB6.

scholarly journals Response of wheat DREB transcription factor to drought stress based on DNA methylation

2020 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Resistance Mechanism ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought stress, and the research on drought resistance mechanism of wheat is very important. Dehydration responsive element binding protein (DREB) plays an important role in the response of plant to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat, their CDS sequences were composed of 732 bp, 837 bp or 1035 bp, respectively, and one 712 bp intron was found in DREB6. Although AP2/EREBP domain of DREB2, DREB6 and Wdreb2 had 73.25% identity, they belong to different types of DREB transcription factor, and the expression of Wdreb2 was significantly higher, yet was the lowest in DREB2. Under drought stress, the expression of DREB2, DREB6 and Wdreb2 could be induced, but had different trends along with the increase of stress time, and their expression had tissue specificity, was obviously higher in leaf. Promoter of DREB2, DREB6 and Wdreb2 in leaf was further studied, some elements related to adverse stress were found, and the promoter of DREB2 and Wdreb2 was slightly methylated, but DREB6 promoter was moderately methylated. Compared with the control, the level of promoter methylation in DREB2 and DREB6 decreased as stressed for 2 h, then increased along with the increase of stress time, which was opposite in Wdreb2 promoter, the status of promoter methylation in DREB2, DREB6 and Wdreb2 also had significant change under drought stress. Further analysis showed that promoter methylation of DREB6 and Wdreb2 was negatively correlated with their expression, especially was significant in Wdreb2. Conclusions: DREB2, DREB6 and Wdreb2 might function differently in response to drought stress, and promoter methylation had more significant effects on gene expression of Wdreb2 and DREB6.

scholarly journals Response of wheat DREB transcription factor to drought stress based on DNA methylation

2020 ◽  
Author(s):  
Yanqiu Zhu ◽  
Huihui Wang ◽  
Wenjing Jia ◽  
Xiaoyan Wei ◽  
Zhikun Duan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Drought Stress ◽  
Promoter Methylation ◽  
Resistance Mechanism ◽  
Dreb Transcription Factor ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background: The growth and development of wheat are seriously influenced by drought stress, and the research on drought resistance mechanism of wheat is very important. Dehydration responsive element binding protein (DREB) plays an important role in the response of plant to drought stress, but epigenetic regulation for gene expression of DREB transcription factor is less studied, especially the regulatory role of DNA methylation has not been reported.Results: In this research, DREB2, DREB6 and Wdreb2 were cloned from wheat, their CDS sequences were composed of 732 bp, 837 bp or 1035 bp, respectively, and one 712 bp intron was found in DREB6. Although AP2/EREBP domain of DREB2, DREB6 and Wdreb2 had 73.25% identity, they belong to different types of DREB transcription factor, and the expression of Wdreb2 was significantly higher, yet was the lowest in DREB2. Under drought stress, the expression of DREB2, DREB6 and Wdreb2 could be induced, but had different trends along with the increase of stress time, and their expression had tissue specificity, was obviously higher in leaf. Promoter of DREB2, DREB6 and Wdreb2 in leaf was further studied, some elements related to adverse stress were found, and the promoter of DREB2 and Wdreb2 was slightly methylated, but DREB6 promoter was moderately methylated. Compared with the control, the level of promoter methylation in DREB2 and DREB6 decreased as stressed for 2 h, then increased along with the increase of stress time, which was opposite in Wdreb2 promoter, the status of promoter methylation in DREB2, DREB6 and Wdreb2 also had significant change under drought stress. Further analysis showed that promoter methylation of DREB6 and Wdreb2 was negatively correlated with their expression, especially was significant in Wdreb2. Conclusions: DREB2, DREB6 and Wdreb2 might function differently in response to drought stress, and promoter methylation had more significant effects on gene expression of Wdreb2 and DREB6.

scholarly journals Response of Wheat DREB Transcription Factor to Osmotic Stress Based on DNA Methylation

2021 ◽  
Vol 22 (14) ◽  
pp. 7670
Author(s):  
Huihui Wang ◽  
Yanqiu Zhu ◽  
Ping Yuan ◽  
Shanglin Song ◽  
Tianyu Dong ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Promoter Methylation ◽  
Tissue Specificity ◽  
Transcript Expression ◽  
Dreb Transcription Factor ◽  
Different Types ◽  
The Status ◽  
Element Binding Protein ◽  
Responsive Element ◽  
Dreb Transcription Factors

Dehydration-responsive element-binding protein (DREB) plays an important role in response to osmotic stress. In this study, DREB2, DREB6 and Wdreb2 are isolated from wheat AK58, yet they belong to different types of DREB transcription factors. Under osmotic stress, the transcript expression of DREB2, DREB6 and Wdreb2 has tissue specificity and is generally higher in leaves, but their expression trends are different along with the increase of osmotic stress. Furthermore, some elements related to stresses are found in their promoters, promoters of DREB2 and Wdreb2 are slightly methylated, but DREB6’s promoter is moderately methylated. Compared with the control, the level of promoter methylation in Wdreb2 is significantly lower under osmotic stress and is also lower at CG site in DREB2, yet is significantly higher at CHG and CHH sites in DREB2, which is also found at a CHG site in DREB6. The status of promoter methylation in DREB2, DREB6 and Wdreb2 also undergoes significant changes under osmotic stress; further analysis showed that promoter methylation of Wdreb2 is negatively correlated with their expression. Therefore, the results of this research suggest the different functions of DREB2, DREB6 and Wdreb2 in response to osmotic stress and demonstrate the effects of promoter methylation on the expression regulation of Wdreb2.

scholarly journals DNA Methylation and Expression Profiles of Whole Blood in Parkinson’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Adrienne R. Henderson ◽  
Qi Wang ◽  
Bessie Meechoovet ◽  
Ashley L. Siniard ◽  
Marcus Naymik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parkinson’S Disease ◽  
Dna Methylation ◽  
Parkinson's Disease ◽  
Transcription Factor ◽  
Whole Blood ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Motor Deficits ◽  
Age Related

Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease. It is presently only accurately diagnosed at an advanced stage by a series of motor deficits, which are predated by a litany of non-motor symptoms manifesting over years or decades. Aberrant epigenetic modifications exist across a range of diseases and are non-invasively detectable in blood as potential markers of disease. We performed comparative analyses of the methylome and transcriptome in blood from PD patients and matched controls. Our aim was to characterize DNA methylation and gene expression patterns in whole blood from PD patients as a foundational step toward the future goal of identifying molecular markers that could predict, accurately diagnose, or track the progression of PD. We found that differentially expressed genes (DEGs) were involved in the processes of transcription and mitochondrial function and that PD methylation profiles were readily distinguishable from healthy controls, even in whole-blood DNA samples. Differentially methylated regions (DMRs) were functionally varied, including near transcription factor nuclear transcription factor Y subunit alpha (NFYA), receptor tyrosine kinase DDR1, RING finger ubiquitin ligase (RNF5), acetyltransferase AGPAT1, and vault RNA VTRNA2-1. Expression quantitative trait methylation sites were found at long non-coding RNA PAX8-AS1 and transcription regulator ZFP57 among others. Functional epigenetic modules were highlighted by IL18R1, PTPRC, and ITGB2. We identified patterns of altered disease-specific DNA methylation and associated gene expression in whole blood. Our combined analyses extended what we learned from the DEG or DMR results alone. These studies provide a foundation to support the characterization of larger sample cohorts, with the goal of building a thorough, accurate, and non-invasive molecular PD biomarker.

scholarly journals Molecular regulation of fetal brain development in pigs

2021 ◽  
Author(s):  
◽  
Monica P. Strawn
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Brain Development ◽  
Early Development ◽  
Expression Patterns ◽  
Fetal Brain ◽  
Molecular Regulation ◽  
Fetal Brain Development ◽  
The Brain

Two experiments were conducted to investigate molecular regulation that impacts fetal brain development in pigs. In the first experiment (Chapter 2), gene expression was profiled by RNA sequencing (RNA-seq) to examine the whole transcriptome of the male (M) and female (F) fetal brain at gestation day (d) 45, 60 and 90. The analysis showed fewer differentially expressed genes (DEGs) in the brain of male and female fetuses in earlier gestation (d45-d60) when compared to late gestation (d60-d90). The homeobox (HOX) A5 gene that regulates pattern formation in early development was in the top upregulated DEGs between d45 to d60 in fetuses of both sexes. This study also found HOX B5 and D3 genes were in the top upregulated genes between d45 and d60 of the fetal brain of females, but not males. The second experiment (Chapter 3) investigated DNA methylation in pigs. DNA methylation in the fetal brain of both sexes at the same three gestation days was performed by enzymatic methyl sequencing (EM-seq). Hotspots of methylation in specific chromosomal regions were observed in the analysis. The analysis identified 1,475 sites in the pig genome that were methylated in the fetal brain, irrespective of sex, during development. The same sites were methylated in a canonically correlated manner in the blood of the adult stage, both in sows and boars. This is consistent with the Dilman theory of developmental aging (DevAge), which suggests that aging and early development of the brain are regulated by common molecular processes. A comparative analysis (Chapter 4) compared the gene expression patterns in the fetal brain and placenta between pigs and mice. The analysis identified 112 genes that were expressed (mean FPKM > 10) in the fetal brain of both species but not expressed (mean FPKM < 1) in the placenta of either species, and 10 genes that were expressed in the placenta of both species but not expressed in the fetal brain. In-silico analysis of the transcription factor binding sites in the 500 bp of the upstream DNA of these common genes revealed that they were commonly regulated by the RE1 silencing transcription factor (REST), which is a multifaceted transcription factor that acts as a master regulator of neurogenesis as well as controls neural excitation and the aging processes.

Expressional Analysis of an EREBP Transcription Factor Gene OsEBP-89 in Rice

2004 ◽  
Vol 36 (1) ◽  
pp. 21-26
Author(s):  
Hui Shen ◽  
Zong-Yang Wang
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Adventitious Roots ◽  
Northern Blot Analysis ◽  
Basal Part ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Element Binding Protein ◽  
Sequence Region ◽  
Responsive Element

Abstract OsEBP-89 gene encodes an ethylene responsive element binding protein (EREBP) transcription factor from rice (Oryza sativa). Northern blot analysis revealed that OsEBP-89 was expressed in root, stem, seeds, flowers and leaves. Histochemical assay showed that β-glucuronidase (GUS) was expressed mainly in phloem of vascular tissues of the root and stem transition region (RST), basal part of sheath roots, stem node and basal part of adventitious roots, also in endosperm of seeds in transgenic rice harboring OsEBP-89/GUS construct (pNSG). A sequence region from –279 to –97 was found to play an important role for OsEBP-89 gene expression through promoter deletion assay. The possible function of OsEBP-89 gene was discussed.

scholarly journals DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon

2021 ◽  
Vol 9 ◽  
Author(s):  
Jolien Diddens ◽  
Louis Coussement ◽  
Carolina Frankl-Vilches ◽  
Gaurav Majumdar ◽  
Sandra Steyaert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factor ◽  
Zebra Finch ◽  
Dosage Compensation ◽  
Expression Patterns ◽  
Song Learning ◽  
Sexually Dimorphic ◽  
Gene Expression Dynamics ◽  
Dimorphic Gene Expression

Song learning in zebra finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.

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