The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato

2021 ◽  
Author(s):  
Peng Tian ◽  
Zeteng Lin ◽  
Dongbo Lin ◽  
Shuangyu Dong ◽  
Jianzi Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Phosphate Starvation ◽  
Methylation Alteration

scholarly journals Methylome analysis reveals an important role for epigenetic changes in the regulation of the Arabidopsis response to phosphate starvation

2015 ◽  
Vol 112 (52) ◽  
pp. E7293-E7302 ◽  
Author(s):  
Lenin Yong-Villalobos ◽  
Sandra Isabel González-Morales ◽  
Kazimierz Wrobel ◽  
Dolores Gutiérrez-Alanis ◽  
Sergio Alan Cervantes-Peréz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcriptional Activation ◽  
Phosphate Starvation ◽  
Limiting Factor ◽  
Expression Of Genes ◽  
Pi Acquisition ◽  
Pi Starvation ◽  
Methylome Analysis ◽  
Methylation Patterns

Phosphate (Pi) availability is a significant limiting factor for plant growth and productivity in both natural and agricultural systems. To cope with such limiting conditions, plants have evolved a myriad of developmental and biochemical strategies to enhance the efficiency of Pi acquisition and assimilation to avoid nutrient starvation. In the past decade, these responses have been studied in detail at the level of gene expression; however, the possible epigenetic components modulating plant Pi starvation responses have not been thoroughly investigated. Here, we report that an extensive remodeling of global DNA methylation occurs in Arabidopsis plants exposed to low Pi availability, and in many instances, this effect is related to changes in gene expression. Modifications in methylation patterns within genic regions were often associated with transcriptional activation or repression, revealing the important role of dynamic methylation changes in modulating the expression of genes in response to Pi starvation. Moreover, Arabidopsis mutants affected in DNA methylation showed that changes in DNA methylation patterns are required for the accurate regulation of a number of Pi-starvation–responsive genes and that DNA methylation is necessary to establish proper morphological and physiological phosphate starvation responses.

scholarly journals Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination

2020 ◽  
Author(s):  
Stevie A. Bain ◽  
Hollie Marshall ◽  
Laura Ross
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Sexual Dimorphism ◽  
Planococcus Citri ◽  
Specific Gene ◽  
Paternal Genome ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide

AbstractSexual dimorphism is exhibited in many species across the tree of life with many phenotypic differences mediated by differential expression and alternative splicing of genes present in both sexes. However, the mechanisms that regulate these sex-specific expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, Paternal Genome Elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. P. citri also has no sex chromosomes and as such both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. In this study we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole genome bisulfite sequencing. We have identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifests as more uniform low-levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq we identified extensive sex-specific gene expression and alternative splicing. We found cis-acting DNA methylation is not directly associated with differentially expressed or differentially spliced genes, indicating a broader role for chromosome-wide trans-acting DNA methylation in this species.

DNA modifications in schizophrenia

2020 ◽  
pp. 177-183
Author(s):  
Ehsan Pishva ◽  
Bart P. F. Rutten
Keyword(s):  
Gene Expression ◽  
Risk Factors ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Epigenetic Modification ◽  
Control Gene ◽  
Dna Modifications ◽  
Genetic And Environmental Factors ◽  
The Brain ◽  
Epigenetic Processes

Interplay between genetic and environmental factors plays a major role in shaping the neurodevelopmental origins of schizophrenia. Epigenetic processes act to dynamically control gene expression and are known to regulate key neurobiological and cognitive processes in the brain. Along with mediating the effects of environmental risk factors on the development of disease, epigenetic processes play a central role in the differentiation and development of the human brain. Therefore, investigating epigenetic variations associated with schizophrenia may shed new light on our understanding about the developmental and environmental origins of schizophrenia. DNA methylation is the best-characterized epigenetic modification, playing a role in regulating gene expression, alternative splicing and other transcriptional processes such as X-chromosome inactivation and genomic imprinting. This chapter discusses the evidence to support a role for DNA modifications in schizophrenia, and highlights the opportunities and challenges of ongoing studies.

scholarly journals Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing

2021 ◽  
Vol 22 (15) ◽  
pp. 8285
Author(s):  
Qi Wang ◽  
Jie Xu ◽  
Xuemei Pu ◽  
Haozhe Lv ◽  
Yanjun Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Genotyping By Sequencing ◽  
Inbred Lines ◽  
Sequencing Data ◽  
Positive Correlation ◽  
Differentially Methylated Genes ◽  
Maize Roots ◽  
Interfering Rna

DNA methylation is important for plant growth, development, and stress response. To understand DNA methylation dynamics in maize roots under water stress (WS), we reanalyzed DNA methylation sequencing data to profile DNA methylation and the gene expression landscape of two inbred lines with different drought sensitivities, as well as two of their derived recombination inbred lines (RILs). Combined with genotyping-by-sequencing, we found that the inheritance pattern of DNA methylation between RILs and parental lines was sequence-dependent. Increased DNA methylation levels were observed under WS and the methylome of drought-tolerant inbred lines were much more stable than that of the drought-sensitive inbred lines. Distinctive differentially methylated genes were found among diverse genetic backgrounds, suggesting that inbred lines with different drought sensitivities may have responded to stress in varying ways. Gene body DNA methylation showed a negative correlation with gene expression but a positive correlation with exon splicing events. Furthermore, a positive correlation of a varying extent was observed between small interfering RNA (siRNA) and DNA methylation, which at different genic regions. The response of siRNAs under WS was consistent with the differential DNA methylation. Taken together, our data can be useful in deciphering the roles of DNA methylation in plant drought-tolerance variations and in emphasizing its function in alternative splicing.

scholarly journals DNA methylation and alternative splicing modulate FBXW11 gene expression in Holstein bull testis and are correlated with sperm quality

BIOCELL ◽  
2021 ◽  
Vol 45 (1) ◽  
pp. 79-87
Author(s):  
YONG LIU ◽  
ZHIHUA JU ◽  
QIANG JIANG ◽  
WENHAO LIU ◽  
CHUNHONG YANG ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Sperm Quality ◽  
Holstein Bull

DNA methylation/hydroxymethylation regulate gene expression and alternative splicing during terminal granulopoiesis

Epigenomics ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 95-109 ◽  
Author(s):  
Dadi Gao ◽  
Natalia Pinello ◽  
Trung V Nguyen ◽  
Annora Thoeng ◽  
Rajini Nagarajah ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing ◽  
Regulate Gene Expression ◽  
Regulate Gene

scholarly journals Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

2020 ◽  
Vol 103 (5) ◽  
pp. 1744-1766 ◽  
Author(s):  
Daniel Niyikiza ◽  
Sarbottam Piya ◽  
Pratyush Routray ◽  
Long Miao ◽  
Won‐Seok Kim ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Alternative Splicing

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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